Merge pull request #5 from yhoogstrate/bp_detect_intronic

Intronic break point detection + installer recipe

.gitignore

@@ -1,3 +1,14 @@
-*.txt
+/*.txt
 *.png
 /samples
+.Rhistory
+tmp/
+/build
+*.pyc
+*.egg-info
+/dist
+/data*/*.swp
+/data
+*.swp
+.coverage
+/htmlcov/*

.travis.yml

@@ -0,0 +1,22 @@
+language: python
+
+python:
+#  - "2.6" << misses pysam 'import sysconfig' => 'ImportError: No module named sysconfig'
+  - "2.7"
+
+# Needs FuMa, which needs HTSeq ported to Py3
+#  - "3.2"
+#  - "3.3"
+#  - "3.4"
+#  - "3.5"
+#  - "3.5-dev" # 3.5 development branch
+#  - "nightly" # currently points to 3.6-dev
+
+install:
+  - pip install -r requirements.txt
+
+script:
+  - nosetests -v tests/*.py
+
+notifications:
+  email: false

bin/dr-disco

@@ -0,0 +1,64 @@
+#!/usr/bin/env python3
+# *- coding: utf-8 -*-
+# vim: set expandtab tabstop=4 shiftwidth=4 softtabstop=4 textwidth=79:
+
+"""
+Dr. Disco
+
+[License: GNU General Public License v3 (GPLv3)]
+ 
+ This file is part of Dr. Disco.
+ 
+ FuMa is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ 
+ Dr. Disco is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+"""
+
+import drdisco
+import click
+
+from drdisco import __version__, __author__, __homepage__
+
+
+def main():
+    CLI()
+
+@click.version_option(__version__)
+@click.group()
+def CLI():
+    pass
+
+
+#@click.command(help="This tool requires the '*.Chimeric.out.sam' files of RNA STAR converted into BAM")
+#@click.argument('bam_file_discordant')
+#@click.argument('bam_file_discordant_fixed')
+@CLI.command(name="fix",short_help="Fixes chimeric SAM/BAM"
+"alignment produced by RNA-STAR")
+@click.option("--temp-dir","-t",type=click.Path(exists=True),default="/tmp",help="Path"
+"in which temporary files will be stored (default: /tmp)")
+@click.argument('output_bam_file')
+@click.argument('input_bam/sam_file', type=click.File('r'))
+def CLI_fix_chimeric_alignment(temp_dir,output_alignment_file,
+    input_alignmentfile):
+    alignment_hande = ChimericAlignment(input_alignmentfile)
+    alignment_handle.convert(output_alignment_file,temp_dir)
+
+
+@CLI.command(name='intronic',short_help='Detects and interprets intronic break points')
+@click.argument('output_file', type=click.File('w'))
+@click.argument('fusion_candidates_input_file', type=click.Path(exists=True))
+@click.argument('bam_input_file', type=click.Path(exists=True))
+def CLI_detect_intronic_break_points(output_file,input_list,input_alignment):
+    pass
+
+if __name__ == '__main__':
+    main()
+

coverage.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+py.test --cov-report html --cov=drdisco tests